Over time = Gradually (is this correct?)Over time, he will learn it = Gradually (on a day by day basis, he will learn English)

Yes, gradually is a pretty good interpretation. "Over time" suggests a period of time that is longer than just a few days or weeks.

Quote:

"Am I not supposed to modify this file?" - Is this a correct sentence?

Yes, that sentence can be used when you originally believed that you were supposed to modify the file and now there is some kind of doubt about that. You are basically asking for clarification of what you are supposed to do.._________________"Nearly all men can stand adversity, but if you want to test a man's character, give him power." ~ Abraham Lincoln